Primary cilia are microtubule-based organelles that are expressed on almost all mammalian cells. It has become apparent that these structures are important signaling hubs that serve crucial roles in Wnt, hedgehog, extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) and Notch signaling pathways. A number of diseases have been found to involve dysfunctional primary cilia; collectively these diseases are called ciliopathies. In recent years, there has been more focus on the association between primary cilia and cancer, including renal, pancreatic and breast cancer. Numerous studies have demonstrated that various types of cancer cells fail to express cilia. Notably, it has also been indicated that a number of renal carcinogens induce a significant loss of cilia in renal epithelial cells. The present review focuses on the existing literature regarding primary cilia and their involvement with cancer signaling pathways, providing a brief overview of the structural features and functions of primary cilia, then discussing the evidence associating primary cilia with cancer, and presenting the available information on the ERK/MAPK, hedgehog and Wnt signaling pathways, and their involvement in primary cilia in association with cancer.